Commit c5b8aa4c authored by Chris Evenhuis's avatar Chris Evenhuis
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parent 114443b5
......@@ -8,7 +8,7 @@
* The clusters were segmented by seed based distance transformed watershed:
- Euclidean Distance Map was calculated for each RoI
- Seed points found as maxima on the distance distance map.
- Marker controlled watershed was performed using the seed points and the distance
- Marker Controlled Watershed [1] was performed using the seed points and the inverted distance transform.
![](media/cluster_seg.png)
......@@ -16,11 +16,12 @@ This create a list of RoIs for each cell. This allowed each cell to assigned to
### Detecting of strings
To identify string structure in the GFP channel, for each cell RoI the following was performed:
To identify string structure in the GFP channel, for each cell RoI and each slice in the Z-stack the following was performed:
- A White Top Hat transformation (MorhphoLibJ [1]) was performed on the GFP channel to enhance string-like features (disk of radius 5px).
- The 16-bit image was converted to 8-bit by setting maximum display range to 4 times the 97th percentile of the intensity distribution.
- Ridge Detect Plugin [2] was run to create RoIs for each filament
- The statistics of each filament (length, width etc) were recorded.
![](media/ridge_detection.png)
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